Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet

Abstract

Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a ‘poor man’s crop’, finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

“…However, it also sheds further light on the evolutionary history of finger millet, revealing diverse pathways of diversification within and between regions. These findings can offer valuable insights to guide future breeding efforts and are in accordance with the other recent work of Devos et al (2023), who used the same genome assembly and genotype-by-sequencing to assess the genomic characteristics of a panel of 294 E. coracana and three E. indica accessions.…”

“…Both wild E. coracana subsp. africana (i.e., the considered most likely immediate progenitor) and a range of other Eleusine species are sympatric with the finger millet crop in southern Africa (Figure 1), providing opportunities for introgression (see also discussion in Devos et al, 2023). This type of process has been observed in other cereals, including wheat (He et al, 2019), and would be consistent with genotyping-by-sequencing in finger millet that has revealed chromosomal rearrangements between sub-genomes (Qi et al, 2018).…”

“…Despite their limited scope, these previous studies revealed localized and regional genetic variation, including differentiation between Africa and Asia, as well as instances of admixture between the two continents. A recent more extensive study by Devos et al (2023) has also confirmed these findings.…”

“…Additionally, future GWA studies may need to consider larger populations with more extensive phenotypic data from multiple locations and higher SNP coverage across the genome, including rare variants, to overcome the limitations in discovering MTAs as was the case in this study. The identification of precise causal genomic regions may remain challenging in finger millet due to the relatively slow decay of LD (although see Devos et al, 2023). Last, as genomic resources continue to develop for finger millet, breeding material selection approaches that assign genomic estimated breeding values to each separate sub-genome may also open a possibility for weighted sub-genome selection.…”

“…The methods for library construction, DArTseq, data generation, and initial output quality control steps were described previously by Sansaloni et al, 2011. The SNP positions were assigned using the v1.1 finger millet genome assembly (https://phytozome-next.jgi.doe.gov/info/ Ecoracana_v1_1), which was recently detailed in the study of Devos et al (2023).…”